Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
25.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.83, Jaccard 0.62
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.561 kcal/mol/HA)
✓ Good fit quality (FQ -5.57)
✓ Good H-bonds (3 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ High strain energy (25.3 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (15)
Score
-18.528
kcal/mol
LE
-0.561
kcal/mol/HA
Fit Quality
-5.57
FQ (Leeson)
HAC
33
heavy atoms
MW
460
Da
LogP
4.64
cLogP
Interaction summary
HB 3
HY 24
PI 0
CLASH 1
Interaction summary
HB 3
HY 24
PI 0
CLASH 1
| Final rank | 1.566 | Score | -18.528 |
|---|---|---|---|
| Inter norm | -0.693 | Intra norm | 0.132 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 3 |
| Artifact reason | geometry warning; 15 clashes; 3 protein contact clashes; moderate strain Δ 25.3 | ||
| Residues |
ALA77
ALA90
ARG74
GLY85
LEU73
LYS211
LYS89
MET70
PHE83
PRO187
PRO212
PRO213
TYR210
VAL88
| ||
Protein summary
493 residues
| Protein target | T16 | Atoms | 7551 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 10 | Native recall | 0.83 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 27 | 1.0529802445936258 | -0.999172 | -29.2925 | 3 | 21 | 0 | 0.00 | - | - | no | Open |
| 26 | 1.3055420784633858 | -0.81686 | -19.118 | 1 | 17 | 0 | 0.00 | - | - | no | Open |
| 9 | 1.5663218808035626 | -0.692956 | -18.528 | 3 | 14 | 10 | 0.83 | - | - | no | Current |
| 21 | 1.9804322200448852 | -0.725206 | -18.4083 | 1 | 16 | 0 | 0.00 | - | - | no | Open |
| 14 | 2.986390587435558 | -0.73263 | -20.6162 | 4 | 22 | 0 | 0.00 | - | - | no | Open |
| 18 | 4.0298560666303 | -0.618302 | -19.1872 | 4 | 11 | 0 | 0.00 | - | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-18.528kcal/mol
Ligand efficiency (LE)
-0.5615kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.571
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
460.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.64
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
130.83kcal/mol
Minimised FF energy
105.58kcal/mol
SASA & burial
✓ computed
SASA (unbound)
790.1Ų
Total solvent-accessible surface area of free ligand
BSA total
534.0Ų
Buried surface area upon binding
BSA apolar
496.7Ų
Hydrophobic contacts buried
BSA polar
37.2Ų
Polar contacts buried
Fraction buried
67.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3338.5Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1491.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)